GeneBe

TRPV5

protein-coding

transient receptor potential cation channel subfamily V member 5, the group of Transient receptor potential cation channels|Ankyrin repeat domain containing

Gene summary

This gene is a member of the transient receptor family and the TrpV subfamily. The calcium-selective channel encoded by this gene has 6 transmembrane-spanning domains, multiple potential phosphorylation sites, an N-linked glycosylation site, and 5 ANK repeats. This protein forms homotetramers or heterotetramers and is activated by a low internal calcium level. [provided by RefSeq, Jul 2008]

Previous symbols:
  • ECAC1

MANE transcript

NM_019841.7

Inheritance

AR

ClinVar variants

P:1U:103B:11

Top phenotype

TRPV5-related disorder

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr7:142,908,101-142,933,746

External References & Databases

Ensembl (ENSG00000127412)NCBI Gene (56302)OMIM (606679)HGNC:3145GenCCUniProt (Q9NQA5)AlphaFoldClinVar (TRPV5)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~25.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hypercalciuria, absorptive, 2LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0007748

Submitter: Ambry Genetics

urinary system disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0002118

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TRPV5 variants in ClinVar

4 Conditions Cataloged
not specifiedTotal: 102
not providedTotal: 9
TRPV5-related disorderTotal: 3
Renal Calcium Wasting HypercalciuriaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_019841.7. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
4
clinvar
 4
missense
1
clinvar
99
clinvar
9
clinvar
2
clinvar
 111
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total1010392115

Highest pathogenic variant AF is 0.000017351751

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_019841.7RefSeqNP_062815.315MANE Select
ENST00000265310.6EnsemblENSP00000265310.115MANE Select
ENST00000439304.5EnsemblENSP00000406361.114Standard
ENST00000442623.1EnsemblENSP00000406572.18Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Endocrine and other factor-regulated calcium reabsorption - Homo sapiens (human)
  • Osteoclast Signaling
  • Vitamin D Receptor Pathway
  • Stimuli-sensing channels
  • Ion channel transport

Biological Process

  • calcium ion transport
  • regulation of urine volume
  • protein tetramerization
  • protein homotetramerization
  • calcium ion homeostasis

Molecular Function

  • ion channel activity
  • calcium channel activity
  • protein binding
  • calmodulin binding
  • metal ion binding

Cellular Component

  • plasma membrane
  • integral component of plasma membrane
  • apical plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000265310
Coding exons
15
Length
25639
Individuals with no LoFs
125672
Homozygous LoFs
0
Heterozygous LoFs
76
Defined
125748
p
0.000302
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.1934464351.030.00002534752
Missense (PolyPhen)129152.050.848391705
Synonymous-1.531941691.150.000009351494
Loss of Function1.682738.20.7070.00000217371

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000370.00037rare
Latino/Admixed American0.000290.00029rare
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish0.000420.00042rare
European (Non-Finnish)0.000300.00030rare
South Asian0.000420.00042rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Constitutively active calcium selective cation channel thought to be involved in Ca(2+) reabsorption in kidney and intestine (PubMed:11549322, PubMed:18768590). Required for normal Ca(2+) reabsorption in the kidney distal convoluted tubules (By similarity). The channel is activated by low internal calcium level and the current exhibits an inward rectification (PubMed:11549322, PubMed:18768590). A Ca(2+)-dependent feedback regulation includes fast channel inactivation and slow current decay (By similarity). Heteromeric assembly with TRPV6 seems to modify channel properties. TRPV5-TRPV6 heteromultimeric concatemers exhibit voltage-dependent gating (By similarity). {ECO:0000250|UniProtKB:P69744, ECO:0000250|UniProtKB:Q9XSM3, ECO:0000269|PubMed:11549322, ECO:0000269|PubMed:18768590}.;

Recessive Scores

pRec
0.294

Intolerance Scores

LoFtool
0.339
RVIS EVS
-0.02
RVIS percentile EVS
52.32

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.773

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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